refactoring Alignment #768
refactoring Alignment #768

Anaphory/beast2,CompEvol/beast2,tgvaughan/beast2,CompEvol/beast2,Anaphory/beast2,Anaphory/beast2,CompEvol/beast2,tgvaughan/beast2,tgvaughan/beast2,CompEvol/beast2,Anaphory/beast2,tgvaughan/beast2